PeptiHub：一个经过精心整理的癌症相关肽的资源库，具有先进的肽探索和发现工具

PeptiHub: a curated repository of precisely annotated cancer-related peptides with advanced utilities for peptide exploration and discovery

Database-The Journal of Biological Databases and Curation

影响因子:3.6

分区:生物学4区 / 数学与计算生物学4区

发表日期:2024 Sep 20

作者: Sara Zareei, Babak Khorsand, Alireza Dantism, Neda Zareei, Fereshteh Asgharzadeh, Shadi Shams Zahraee, Samane Mashreghi Kashan, Shirin Hekmatirad, Shila Amini, Fatemeh Ghasemi, Maryam Moradnia, Atena Vaghf, Anahid Hemmatpour, Hamdam Hourfar, Soudabeh Niknia, Ali Johari, Fatemeh Salimi, Neda Fariborzi, Zohreh Shojaei, Elaheh Asiaei, Hossein Shabani

DOI: 10.1093/database/baae092

摘要

Peptihub（https://bioinformaticscollege.ir/peptihub/）是一个经过细致整理、基于科学文献记录的癌症相关肽（CRPs）资源库。该资源库包含多样的CRPs，展示了广泛的效果和活性。一些肽显示出显著的抗癌效果，另一些则无明显影响，甚至具有非药物功能，包括药物载体或致癌特性。目前，Peptihub收录了874个CRPs，覆盖10个不同的生物体类别、26个器官和438个细胞系。每个条目都配备了易于访问的三维构象数据，来源于实验或预测方法。用户可以通过基础、高级和BLAST序列搜索三种方式进行查询。此外，肽的详细注释允许用户根据其特定活性（抗癌、无效、无显著效果、致癌等）和在癌症条件下的有效性（比例和IC50）进行探索，特别是在不同器官中。这一特性便于构建稳健的训练和测试数据集。此外，PeptiHub提供1141个特征，用户可以选择最相关的特征以满足其研究需求。特征包括aaindex1（分为六个主要子类别：α-倾向性、β-倾向性、组成指数、疏水性、理化性质和其他性质）、氨基酸组成（Amino acid Composition和Dipeptide Composition）以及分组氨基酸组成（Grouped amino acid composition、Grouped dipeptide composition和Conjoint triad类别）。这些工具不仅加快了基于机器学习的肽设计，还促进了肽的分类。数据库网址： https://bioinformaticscollege.ir/peptihub/。

Abstract

Peptihub (https://bioinformaticscollege.ir/peptihub/) is a meticulously curated repository of cancer-related peptides (CRPs) that have been documented in scientific literature. A diverse collection of CRPs is included in the PeptiHub, showcasing a spectrum of effects and activities. While some peptides demonstrated significant anticancer efficacy, others exhibited no discernible impact, and some even possessed alternative non-drug functionalities, including drug carrier or carcinogenic attributes. Presently, Peptihub houses 874 CRPs, subjected to evaluation across 10 distinct organism categories, 26 organs, and 438 cell lines. Each entry in the database is accompanied by easily accessible 3D conformations, obtained either experimentally or through predictive methodology. Users are provided with three search frameworks offering basic, advanced, and BLAST sequence search options. Furthermore, precise annotations of peptides enable users to explore CRPs based on their specific activities (anticancer, no effect, insignificant effect, carcinogen, and others) and their effectiveness (rate and IC50) under cancer conditions, specifically within individual organs. This unique property facilitates the construction of robust training and testing datasets. Additionally, PeptiHub offers 1141 features with the convenience of selecting the most pertinent features to address their specific research questions. Features include aaindex1 (in six main subcategories: alpha propensities, beta propensity, composition indices, hydrophobicity, physicochemical properties, and other properties), amino acid composition (Amino acid Composition and Dipeptide Composition), and Grouped Amino Acid Composition (Grouped amino acid composition, Grouped dipeptide composition, and Conjoint triad) categories. These utilities not only speed up machine learning-based peptide design but also facilitate peptide classification. Database URL: https://bioinformaticscollege.ir/peptihub/.